GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluB in Lactobacillus silagei IWT126

Align GluB aka CGL1951, component of Glutamate porter (characterized)
to candidate WP_054653754.1 CES79_RS00810 transporter substrate-binding domain-containing protein

Query= TCDB::P48242
         (295 letters)



>NCBI__GCF_002217945.1:WP_054653754.1
          Length = 277

 Score =  109 bits (272), Expect = 8e-29
 Identities = 85/276 (30%), Positives = 134/276 (48%), Gaps = 16/276 (5%)

Query: 4   KRTFTRIGAILGATALAGVTLTACGDSSGGDGFLA--AIENGSVNVGTKYDQPGLGLRNP 61
           K+ F  +  I+ + AL  + LTACG     D  +   A ++ ++  G K D    GL + 
Sbjct: 2   KKLFRLVSVIVSSLALL-LVLTACGSKPLADQNVVTRAKQSNTITWGVKADTKLFGLMDV 60

Query: 62  DNS-MSGLDVDVAEYVVNSIADDKGWDHPTIEWRESPSAQRETLIQNGEVDMIAATYSIN 120
            NS + G +VD+A+ +   I   KG      ++ +  S+ R  L++NG +D I AT +I 
Sbjct: 61  KNSQIKGFEVDMAKALTKQILGPKG----KADFVQVTSSTRMPLLKNGNIDAIMATMTIT 116

Query: 121 AGRSESVNFGGPYLLTHQALLVRQDDDRIETLEDLD-NGLILCSVSGSTPAQKVKDVLPG 179
             R + V+F   Y    Q+LLV+ +   I+ ++DL+ NG  +  V GS   Q V    P 
Sbjct: 117 PERLKQVDFSRSYFDAGQSLLVK-NGSPIKNVKDLNKNGATVLGVVGSNSVQNVAKFAPK 175

Query: 180 VQLQEYDTYSSCVEALSQGNVDALTTDATILFGYSQQYEGDFRVVEMEKDGEPFTDEYYG 239
            ++ +   Y+  + AL  G  +ALTTD  IL G S +  G          G  FT E YG
Sbjct: 176 AKVLQLSDYAQAMTALKSGQGEALTTDNGILAGMSVENPG------YHLAGGAFTKEPYG 229

Query: 240 IGLKKDDQEGTDAINAALERMYADGTFQRLLTENLG 275
           I + K+  E    +N AL ++   G + R+L +  G
Sbjct: 230 IAINKNQPEFKHDLNHALTKVEQSGQYNRILKKWFG 265


Lambda     K      H
   0.312    0.133    0.378 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 175
Number of extensions: 7
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 295
Length of database: 277
Length adjustment: 26
Effective length of query: 269
Effective length of database: 251
Effective search space:    67519
Effective search space used:    67519
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory